PINDEL2VCF¶
Convert pindel output to vcf.
Software dependencies¶
- pindel ==0.2.5b8
Example¶
This wrapper can be used in the following way:
rule pindel2vcf:
input:
ref="genome.fasta",
pindel="pindel/all_{type}"
output:
"pindel/all_{type}.vcf"
params:
refname="hg38", # mandatory, see pindel manual
refdate="20170110", # mandatory, see pindel manual
extra="" # extra params (except -r, -p, -R, -d, -v)
log:
"logs/pindel/pindel2vcf.{type}.log"
wrapper:
"0.19.2/bio/pindel/pindel2vcf"
Note that input, output and log file paths can be chosen freely. When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
import os
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("pindel2vcf {snakemake.params.extra} -p {snakemake.input.pindel} -r {snakemake.input.ref} -R {snakemake.params.refname} -d {snakemake.params.refdate} -v {snakemake.output[0]} {log}")